Cloud of Darkness
by Wolfen-Ways
Summary: Giovanni, leader of Team Rocket, remembers the Pokemon, Mewtwo, after seeing files of the clone. Will Ash have to save Mewtwo again before falling into Giovanni's evil hands?
1. Mewtwo's Story

Hello! This is my first Pokemon fic. I always wondered what would happen after the movie, Mewtwo Returns. What if Giovanni remembered little by little of Mewtwo after he wiped out Giovanni's memory? Read on, and find out. This first chapter is in Mewtwo's POV.

**Disclaimer**: I own nothing but the story. Thank you.

I am Mewtwo. I am unlike other Pokemon. This is my story. A team of scientists working to create the world's most powerful living Pokemon discovered a fossilized remnant of Mew, and from it created me.

_"Radio Giovanni's helicopter!" a scientist cried after the glass that held me shattered from my powers. "Tell him what's happened!"_

_"Quiet!" the head scientist retorted. "Let us hear its psychic powers." _

Soon, the Team Rocket leader, who had ordered my creation, trained me to control my abilities. But he viewed me solely as his personal property.

_"You were created by humans to obey humans," he told me, while I just destroyed the armor that held me captive._

_"I was not born a Pokemon," I replied, flying up into the air. "I was created. And my creators have used and betrayed me. So, I stand alone!"_

After destroying his laboratory, I created my own. I lured Pokemon trainers to my island fortress to capture their Pokemon and wreak vengeance on humans. I seized their Pokemon and cloned them, as I had been cloned from Mew. But soon, I encountered my nemesis.

A great battle ensued. A battle to determine who would rule: The Pokemon born into this world or the cloned Pokemon created in mine. The clashes were brutal, and as Mew and I summoned all our strength for one final confrontation, the young trainer cried out for the fighting to cease.

_"Stop!" Ash cried, racing into the center of the explosion._

His selfless actions puzzled me. He was a human who valued all Pokemon, whether born or created. Our battling ceased. Finally, my eyes had been opened, as had my heart.

Then, after the clones and I finally found a place to live in peace, that peace was shattered. Giovanni had found me again.

_"If you continue to defy us, your fellow creations will be used in our experiments, and will certainly leave this world." _I went into the machines that he created, but the human who had saved me before saved me yet again, along with his friends. I had to help him out, so I used the last of my powers to destroy the machines. Ash helped me by throwing me into the lake to heal me. Moving the lake and spring beneath Mount Caina, I told the human that he would forget everything he saw. They reassured me, so I only wiped out the memory of Giovanni and his troops. Now, I have found a place to live on my own, but I fear that Giovanni may be after me once more.

Was this a good start? The last part I added on, so don't get mad at me if it's not good.

Review, please!


	2. Memories

Hello, great people of the fan fiction kingdom! The second chapter of Cloud of Darkness is now underway! Mewtwo now lives his own life in a far off city, while Giovanni lays in his lair, wondering about something. What is the villain thinking of? Read on, and find out!

**Disclaimer**: I own nothing but the story. Thank you.

Giovanni, the leader of Team Rocket, a group of people who steal Pokemon, sat in the middle of his lab, deep in thought. Only a few months ago, he had a strange feeling that he had been defeated by something. He couldn't remember a thing after what Mewtwo did to him. He had no recollection of the psychic Pokemon, or of creating him in the first place.

"Why are these strange feelings coming across me?" he whispered, his agent, 009, coming up to him.

"Sir, I found this," she whispered, holding up a file with a few papers jutting out. "It seems to contain valuable information on a rare Pokemon." Giovanni opened it, and saw a diagram of a Pokemon drawn on it. It had a cat-like body, but stood on its hind legs. A small semi-circle was on the back of its neck, and it appeared to have two demon horns on its head. Under the drawing was the name, "Mewtwo".

"Where have I heard that name before?" Giovanni asked, pounding his desk in frustration.

"Shall I run a scan on the satellite in search of this 'Mewtwo'?" Domino asked him, holding up a black tulip. Giovanni nodded, and Domino raced off, the black tulip falling to the ground.

-**In a far off city**-

The buildings glowed a grey light beneath the sunlight. A cloaked figure stood in the light, but stayed in the shadows of his empty home. It was Mewtwo, the Pokemon that Giovanni saw in the diagram.

"Now, my clones and I live our own lives in this new world," Mewtwo muttered from under the hood. "But, for some reason, I feel a strange presence around me. It is as if someone is searching for me." The Pokemon shook its head, and looked out at the city, a few men in black suits with a large red, "R" on the front storming into the city.

This looks bad for Mewtwo. Why could those Rocket grunts be in the city anyway? Find out in chapter three, Captured.

Review please.


	3. Captured

I'm very sorry about the long wait, but the third chapter of Cloud of Darkness is now underway! Team Rocket has invaded the city that Mewtwo inhabits in secrecy. Can he escape the clutches of the Rocket soldiers before they find him? Read on, and find out!

**Disclaimer**: I own nothing but the story. Thank you.

Mewtwo looked down at the crowded city streets, many citizens screaming in fear from the Rocket soldiers that stormed the brightly lit city, their shadows casting dark forms on the buildings and sidewalks. The Pokemon pulled up the hood of its cloak over its head, its eyes casting a blue glow as it generated its telekinesis. The door behind him burst onto the floor, five Rocket soldiers standing in the fallen doorway, grasping Poke Balls tightly in their gloved hands.

"We of Team Rocket are searching for the Pokemon Mewtwo, and we have heard that he is in this city," muttered one. "Have you seen him?" The concealed Pokemon lifted a covered paw, and shot a bright blue blast straight at the soldiers, knocking them over like dominos. It hovered into the air, and glided out the window, the Rocket soldiers following below it.

"Send out your Pokemon, now!" shouted one to the others. Poke Balls flew up into the air, and many Pokemon filled the air, chasing after the hidden Mewtwo. He continuously shot blue energy at the Pokemon, knocking them backwards as he tried to get away. He landed on the ground, but was soon surrounded by the Rockets, Giovanni included.

"Well, this certainly is a surprise," the leader muttered. "I have found you at last."

"How can you remember me?" Mewtwo inquired harshly. "I erased your memory back in the Johto Region!"

"It seems that one of my agents found a drawing of you, and ran a satellite search for you. Now, you are going to be mine once more!"

"We will see about that," Mewtwo replied coldly. "I warn you, my strength has become far more greater then when we met before." All around the Pokemon, the Rocket soldiers aimed bazookas at him, preparing to fire.

"FIRE!" Giovanni shouted, the soldiers shooting stun powder at the Pokemon. It was too much for the Psychic Pokemon to bare. Its hood fell off of its face as it landed on the dust barren ground, unmoving. Giovanni grinned as a net surrounded the stunned creature, a helicopter whirring overhead. A ladder lowered itself near the leader, the net rising along with the helicopter.

"You will soon be mine to control the world, Mewtwo," Giovanni laughed as the copter took off into the grey skies, the net dangling below towards the city. Mewtwo opened one bleary eye, gazing down at its home.

"No…" it muttered before falling unconscious once again.

This doesn't look good. What will Giovanni do with the psychic Pokemon? Find out in chapter four, The Dark Clone.

Review please!


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